Job ID = 2001712 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,136,259 reads read : 21,136,259 reads written : 21,136,259 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:10 21136259 reads; of these: 21136259 (100.00%) were unpaired; of these: 479316 (2.27%) aligned 0 times 15684207 (74.21%) aligned exactly 1 time 4972736 (23.53%) aligned >1 times 97.73% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1309252 / 20656943 = 0.0634 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 09:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 09:43:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:43:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 09:43:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:43:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 09:43:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:43:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:44:02: 1000000 INFO @ Fri, 05 Jul 2019 09:44:02: 1000000 INFO @ Fri, 05 Jul 2019 09:44:06: 1000000 INFO @ Fri, 05 Jul 2019 09:44:08: 2000000 INFO @ Fri, 05 Jul 2019 09:44:10: 2000000 INFO @ Fri, 05 Jul 2019 09:44:13: 2000000 INFO @ Fri, 05 Jul 2019 09:44:15: 3000000 INFO @ Fri, 05 Jul 2019 09:44:17: 3000000 INFO @ Fri, 05 Jul 2019 09:44:20: 3000000 INFO @ Fri, 05 Jul 2019 09:44:21: 4000000 INFO @ Fri, 05 Jul 2019 09:44:24: 4000000 INFO @ Fri, 05 Jul 2019 09:44:27: 4000000 INFO @ Fri, 05 Jul 2019 09:44:27: 5000000 INFO @ Fri, 05 Jul 2019 09:44:31: 5000000 INFO @ Fri, 05 Jul 2019 09:44:33: 6000000 INFO @ Fri, 05 Jul 2019 09:44:35: 5000000 INFO @ Fri, 05 Jul 2019 09:44:38: 6000000 INFO @ Fri, 05 Jul 2019 09:44:40: 7000000 INFO @ Fri, 05 Jul 2019 09:44:42: 6000000 INFO @ Fri, 05 Jul 2019 09:44:46: 8000000 INFO @ Fri, 05 Jul 2019 09:44:46: 7000000 INFO @ Fri, 05 Jul 2019 09:44:50: 7000000 INFO @ Fri, 05 Jul 2019 09:44:52: 9000000 INFO @ Fri, 05 Jul 2019 09:44:53: 8000000 INFO @ Fri, 05 Jul 2019 09:44:57: 8000000 INFO @ Fri, 05 Jul 2019 09:44:58: 10000000 INFO @ Fri, 05 Jul 2019 09:45:01: 9000000 INFO @ Fri, 05 Jul 2019 09:45:05: 9000000 INFO @ Fri, 05 Jul 2019 09:45:05: 11000000 INFO @ Fri, 05 Jul 2019 09:45:08: 10000000 INFO @ Fri, 05 Jul 2019 09:45:11: 12000000 INFO @ Fri, 05 Jul 2019 09:45:12: 10000000 INFO @ Fri, 05 Jul 2019 09:45:16: 11000000 INFO @ Fri, 05 Jul 2019 09:45:19: 13000000 INFO @ Fri, 05 Jul 2019 09:45:19: 11000000 INFO @ Fri, 05 Jul 2019 09:45:23: 12000000 INFO @ Fri, 05 Jul 2019 09:45:25: 14000000 INFO @ Fri, 05 Jul 2019 09:45:27: 12000000 INFO @ Fri, 05 Jul 2019 09:45:31: 13000000 INFO @ Fri, 05 Jul 2019 09:45:31: 15000000 INFO @ Fri, 05 Jul 2019 09:45:34: 13000000 INFO @ Fri, 05 Jul 2019 09:45:37: 16000000 INFO @ Fri, 05 Jul 2019 09:45:38: 14000000 INFO @ Fri, 05 Jul 2019 09:45:42: 14000000 INFO @ Fri, 05 Jul 2019 09:45:43: 17000000 INFO @ Fri, 05 Jul 2019 09:45:45: 15000000 INFO @ Fri, 05 Jul 2019 09:45:49: 15000000 INFO @ Fri, 05 Jul 2019 09:45:49: 18000000 INFO @ Fri, 05 Jul 2019 09:45:53: 16000000 INFO @ Fri, 05 Jul 2019 09:45:55: 19000000 INFO @ Fri, 05 Jul 2019 09:45:56: 16000000 INFO @ Fri, 05 Jul 2019 09:45:58: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:45:58: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:45:58: #1 total tags in treatment: 19347691 INFO @ Fri, 05 Jul 2019 09:45:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:45:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 09:45:58: #1 tags after filtering in treatment: 19347530 INFO @ Fri, 05 Jul 2019 09:45:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:45:58: #1 finished! INFO @ Fri, 05 Jul 2019 09:45:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:46:00: 17000000 INFO @ Fri, 05 Jul 2019 09:46:03: #2 number of paired peaks: 75115 INFO @ Fri, 05 Jul 2019 09:46:03: start model_add_line... INFO @ Fri, 05 Jul 2019 09:46:04: start X-correlation... INFO @ Fri, 05 Jul 2019 09:46:04: 17000000 INFO @ Fri, 05 Jul 2019 09:46:04: end of X-cor INFO @ Fri, 05 Jul 2019 09:46:04: #2 finished! INFO @ Fri, 05 Jul 2019 09:46:04: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 09:46:04: #2 alternative fragment length(s) may be 4,134,504 bps INFO @ Fri, 05 Jul 2019 09:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.05_model.r INFO @ Fri, 05 Jul 2019 09:46:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:46:07: 18000000 INFO @ Fri, 05 Jul 2019 09:46:12: 18000000 INFO @ Fri, 05 Jul 2019 09:46:15: 19000000 INFO @ Fri, 05 Jul 2019 09:46:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:46:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:46:18: #1 total tags in treatment: 19347691 INFO @ Fri, 05 Jul 2019 09:46:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:46:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 09:46:18: #1 tags after filtering in treatment: 19347530 INFO @ Fri, 05 Jul 2019 09:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:46:18: #1 finished! INFO @ Fri, 05 Jul 2019 09:46:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:46:19: 19000000 INFO @ Fri, 05 Jul 2019 09:46:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:46:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:46:21: #1 total tags in treatment: 19347691 INFO @ Fri, 05 Jul 2019 09:46:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:46:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 09:46:22: #1 tags after filtering in treatment: 19347530 INFO @ Fri, 05 Jul 2019 09:46:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:46:22: #1 finished! INFO @ Fri, 05 Jul 2019 09:46:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:46:23: #2 number of paired peaks: 75115 INFO @ Fri, 05 Jul 2019 09:46:23: start model_add_line... INFO @ Fri, 05 Jul 2019 09:46:23: start X-correlation... INFO @ Fri, 05 Jul 2019 09:46:23: end of X-cor INFO @ Fri, 05 Jul 2019 09:46:23: #2 finished! INFO @ Fri, 05 Jul 2019 09:46:23: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 09:46:23: #2 alternative fragment length(s) may be 4,134,504 bps INFO @ Fri, 05 Jul 2019 09:46:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.20_model.r INFO @ Fri, 05 Jul 2019 09:46:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:46:27: #2 number of paired peaks: 75115 INFO @ Fri, 05 Jul 2019 09:46:27: start model_add_line... INFO @ Fri, 05 Jul 2019 09:46:27: start X-correlation... INFO @ Fri, 05 Jul 2019 09:46:27: end of X-cor INFO @ Fri, 05 Jul 2019 09:46:27: #2 finished! INFO @ Fri, 05 Jul 2019 09:46:27: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 09:46:27: #2 alternative fragment length(s) may be 4,134,504 bps INFO @ Fri, 05 Jul 2019 09:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.10_model.r INFO @ Fri, 05 Jul 2019 09:46:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:47:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:47:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:47:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.05_summits.bed INFO @ Fri, 05 Jul 2019 09:47:44: Done! pass1 - making usageList (56 chroms): 3 millis pass2 - checking and writing primary data (4128 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.20_summits.bed INFO @ Fri, 05 Jul 2019 09:48:04: Done! pass1 - making usageList (25 chroms): 2 millis pass2 - checking and writing primary data (96 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102019/ERX102019.10_summits.bed INFO @ Fri, 05 Jul 2019 09:48:10: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (875 records, 4 fields): 3992 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。